There is a program called Sakasa Mouse which will rotate mouse movement independently of the display. Originally intended as a joke program, but it's just what you need for a touchpad with a rotated display. Another program, EeeRotate, integrates this with iRotate for easy one-step use. Originally designed for the EeePC, but works on every laptop/netbook I've tried it on. Google for EeeRotate for download locations.

To clarify, Sakasa Mouse is used to reverse the mouse rotation that is apparently done by the display driver and which cannot be easily disabled.